Whispers In The Dark
by sniperpal
Summary: Sonic and his friends have always battled Eggman to defend the Earth from his tyranny, but that matters little when an alien army drops out of space and makes all their fighting pointless. These new enemies are without fear, without hesitation, and without mercy. But Earth does not stand alone in this dark hour... (A re-imagining of the Shadow the Hedgehog game. Read/Review please)
1. Danger's Approach

_After some serious decision making, I decided to scrap my last Sonic fic and start this new one. For those of you who read the first WITD, the premise and a few of the OCs will return, but the story in general has been revamped to more closely resemble the Sonic the Hedgehog games. No Sonic comic references, no super long chapters or confusing casts of characters; this will be a straightforward, honest story, and hopefully one hell of an epic ride._

_As you may have guessed, this story was inspired by the song of the same name, although the nightcore version fits the mood of this story more accurately. See if you can figure out where the theme fits into the story before I eventually reveal it. _

_First couple chapters will be kind of short- the story's setup, if you will. The real action will kick off around Chapter Three, if I've planned this correctly. If nothing else, please at least read till there, and then stop if you're still not hooked. The rating will never rise above T, and the content will NOT violate that rating._

_This story contains modified elements of the Shadow the Hedgehog game, as well as my own original ideas. Sonic and Co. belong to Sega. All Specters, Dracs, and Locrun are my OCs. (Those names will make sense later.)_

_Enjoy!_

Danger's Approach

_CLANG! CLANG! CLANG! CLANG!_

The echoing noise of working machinery was audible even on the top floors of the massive fortress, making Dr. Eggman grit his teeth in annoyance. He hated the noisy hours when the robot factories below were active. He hated the mountains around the fortress that trapped the foul air emanating from his machines in the valley, creating a dirty miasma that clouded the view from the large window he stood in front of.

But most of all, he hated that _infernal _hedgehog.

Not a week ago, Sonic and his friends had dealt Eggman one of his most crushing defeats yet, destroying an entire army of his robots, freeing most of the prisoners he had quietly kidnapped, and demolishing his island fortress in the Pacific with a weapon provided for them by G.U.N. Sonic himself had single-handedly brought the doctor's carrier ship down after boarding it on the ground, and Eggman had barely escaped in his personal transport. It had been a humiliating defeat, as well as a massive setback to his plans. The one piece of good news was that he had not been pursued after that, and he had gotten away with a small, unorganized mess of ships, robots, and prisoners.

_For all the good that does me, _Eggman thought, his mustache twitching as he gazed across the smoky valley with a scowl. _My resources are all but gone. My previous army lies in ruins. This other project will take far longer to even begin testing on, let alone reaching the desired results. And the prisoners…_

He had been planning on building a new series of robots- machines piloted by brainwashed humans, which had all proven far more effective than his standard combat robots when the doctor had begun testing his latest inventions. If only he had been given more time to perfect the systems…

But no, that damnable hedgehog and his friends had gotten wind of his plan after the disappearances had been noticed. What few working human-piloted machines he had managed to build were defeated after a lengthy battle with Sonic- and the speedy blue hedgehog would have won far sooner if he had not taken care to save each and every one of the brainwashed people controlling the robots. Sonic the Hedgehog, ever the gallant hero. The thought incensed Doctor Eggman immensely.

And then Sonic had chased Eggman down and defeated him- _again. _Just like every other one of their conflicts. It was slowly driving the doctor insane.

"Good afternoon, Doctor!" a nasally mechanical voice called out from behind him, bringing Eggman out of his funk. The doctor sneered with annoyance as he turned to see his two personal assistants, Orbot and Cubot, rolling through the door of the large office. The machines came to a halt and popped open almost simultaneously, the robots' geometric bodies straightening upright and their large blue eyes flaring to life.

"Doctor, the new project's first batch has been completed down in the factories below," Orbot said. "Would you like to go check on their quality? I promise you will be more than satisfied with the results."

"Hell, I reckon he'll be happier'n a raccoon in a chicken coop!" Cubot exclaimed. The cube-shaped robot's faulty voice chip was stuck on a hillbilly accent today, it seemed. "It's exactly what ya'll were hoping for, Eggman, yes sir! We've got a mighty fine build-up ready for that plan of yours!"

Doctor Eggman snorted. "I have no interest in the first phase products, you fools. The end results are what will require my personal attention. _If _we have the luxury of even reaching that point." He turned his glare away from the two robots, looking out over the smog-filled valley and the many structures surrounding his fortress. Most of the buildings were hangars or warehouses, housing his numerous robotic troops as well as the various ships of his mighty Egg Fleet, but others were prisons- built to prevent the remaining captives inside from escaping or being detected by the outside world.

While keeping them contained was somewhat taxing on what resources he had left, Eggman could not just let them go, even if his plan to use them as pilots for his war machines had failed with no hope of recovery. Letting potential labor and test subjects simply leave would have been the height of folly. And if they happened to be useful for the new project after all, well…

A small, nasty leer spread across Eggman's face as he contemplated Sonic's expression at seeing the possible results of his latest plan. While the doctor wasn't foolish enough to believe it would be easy to accomplish, the project had the potential to utterly destroy Sonic the Hedgehog once and for all. He was certain of it.

Orbot noticed Eggman spacing off again- no doubt daydreaming about his future "conquests"- and the robot pointedly coughed, bringing the doctor's attention back to the machines. "As excited as we are for your… assured future success," Orbot muttered, choosing his words carefully to avoid angering Eggman at all, "there is one more thing that should be brought to your attention, doctor. You might want to step onto the roof for a moment."

"The roof?" Eggman asked, curious but unconcerned. "No thank you, Orbot, but I would much prefer to stay inside, away from that stinking fog out there. What's the issue?"

"That's kinda the point there, boss," Cubot cut in. "That fog from the factories? It's sorta muckin' up the atmosphere. Like, _really_ bad. A lot worse than what we normally see 'round the factories and stuff."

Eggman's brow furrowed in annoyance. "If you're seriously about to berate me for _pollution_ of all things, you two, you had better-"

"Sir, the whole sky has turned red," Cubot cut him off. Eggman was somewhat shocked at the robot's gall- the machines certainly weren't brave enough to speak over him- and it was this breach of character that convinced the doctor that they were serious. "It's like the atmosphere's bleeding; I've never seen anything like it. The new project's materials apparently have a dramatically larger effect on the local environment than you anticipated."

The doctor stared at the two robots for a moment, mustache twitching in annoyance, before sighing and striding across the room towards the door. "Very well," he said, "I'll assess the situation. Environmental damage is one thing, but I'll draw the line at making my own lair uninhabitable."

The five-minute elevator ride to the roof passed quickly, with Eggman engrossed in his thoughts and plans while the two robots bickered about one thing or another. As it was ending, though, the smell of the factories' waste that permeated the air started filtering into the lift, making Eggman wrinkle his nose in distaste. He started taking shallower breaths and refrained from inhaling through his nose as the doors opened and he stepped onto the roof of his fortress, Orbot and Cubot hopping alongside him. The doctor lifted his gaze to the sky, expecting to see a simple red haze over the land.

His mouth opened a little in shock at what he saw.

A huge, swirling mass of red clouds was spiraling low overhead, far closer to the ground than most normal clouds ever were. The entire valley and much of the land surrounding it lay under a dark shadow cast by the crimson sky, the sun having been blotted out by the phenomenon. It was like someone had thrown an ocean of blood-red dye into a hurricane and sent it to hover above his hideout. The freak storm- if it _was _a storm- was not accompanied by wind or rain or any other natural weather. The red clouds simply churned in a seething multitude as three pairs of eyes watched from the roof of the fortress below.

"You fools…" Eggman muttered under his breath. "As if we are capable of causing anything like _that_…"

"Excuse me, Doctor, sir?" Orbot asked? "What was that?"

"Direct our remaining satellites to focus on this area, and send a probe into those clouds," the doctor growled. "Find out what the hell is going on up there! Now!" His furious tone left no room for argument; the two robots nearly scrambled over each other in their race to get back inside the building and carry out his orders. Eggman didn't even notice them leave, however; his mind was racing furiously, trying to remember where he had seen information about this phenomenon.

And he _had _seen something, he was sure of it. The memory was right on the edge of his mind, a blur of documents from a database he almost never accessed anymore…

_Gerald._

His grandfather, Gerald Robotnik- the man who had created Shadow the Hedgehog, the man whose thirst for vengeance against the killers of his granddaughter had nearly brought an end to the world. The little information Eggman had obtained aboard the Space Colony ARK had, in his opinion, been an inheritance from Gerald, and somewhere in that treasure trove of data there had been a mention of red skies appearing when… _something _happened.

_What was it?_ Eggman thought, struggling to remember. _What was the message he left about this…?_

In a moment of sickening clarity, it all came back to the doctor in one sudden, horrifying rush, even as the muted light of the smoke-filled valley suddenly changed, a bright blue glow illuminating everything around him.

_Not a message. A warning._

Doctor Eggman could only look back up at the reddened sky in fear as the first pillar of electric-blue energy descended towards him in a crackling, roaring rush, the resulting explosion tearing the valley apart and lighting the red sky up for miles all around.

* * *

><p><em>Six hours later…<em>

* * *

><p>The black smoke billowing across the sky blocked out most of the mass of red clouds swirling overhead, but the odd phenomenon was still somewhat visible as it hung over the remains of the scorched and smoldering remains of Eggman's mountain hideaway. It became much more prominent, however, when a huge gust of wind suddenly blew over the peak of one of the mountains that surrounded the destroyed valley, the smoke getting blown apart and dissipating in seconds.<p>

As he slowed from an incredibly high speed to a stop, kicking up rocks and dirt and sending it all cascading over the edge of the cliff he ran along, Sonic the Hedgehog spent a few moments taking in the entire scene- the swirling red vortex overhead, the scorched mountains and burning forests that were all that was left of the valley, and the smoldering, scattered wreckage and rubble of the buildings that had made up Eggman's hideout here.

Smoke began blowing in his direction again, and Sonic held a gloved hand over his mouth as he coughed, the light breeze that ruffled his blue fur doing little to dissipate the clouds of black smoke that rose from the ruins of the fortress below. The smell was awful- whatever Eggman had been producing in his factories was all burning now in a series of roaring infernos, fumes and filth getting thrown into the air and spread all over the place by the air currents. Also, though he desperately hoped he was wrong about the source, Sonic was aware of a stinking scent like burnt, greasy meat, only a hundred times worse.

He wasn't going to fool himself into thinking anyone had survived down in the valley, not with the widespread destruction and ruin of the entire fortress and everything around it plainly visible from the cliff he stood on. After racing here as soon as Tails had informed him about the massive explosions that had been going off for hours, trying to convince himself that he hadn't been too late would only make it harder to handle. But to think about the people he had devoted himself to saving, burning alive in the prisons that confined them…

_All those people Eggman was keeping prisoner…_ Sonic thought to himself, their fate hitting him in the gut like a ton of bricks. _We couldn't save them all the last time we fought him, and now, because we failed…_

The hedgehog shook himself mentally, refusing to think that way. Whatever crazy disaster had happened here was most likely the fault of Eggman; a horrific accident, perhaps, or an attempt to go into hiding for good and cover his tracks. The reddened sky overhead had to be a result of the incident as well. There was nothing left to be done there; all Sonic could do now was keep chasing Eggman. He was certain the doctor had survived, just like he always did. Sonic would simply run him down again.

But this time, there would be a price for Eggman to pay.

As Sonic started walking back down the mountainside, the weight of the deaths heavy on him, the drone of a biplane engine became audible and grew louder with every second, causing the hedgehog to look up and search for the _Tornado_, the plane that he and Tails shared. The biplane blew through the thick clouds of smoke that were still rising from the valley floor and landed, skidding to a stop only fifty or so yards away from Sonic. The two-tailed fox in the pilot's seat jumped out, landing on his knees and a hand before running up to Sonic, his eyes huge with terror and worry.

"Sonic, I saw the valley from above," Tails said in a shaky voice, the fur on his tails standing on end. "We need to get down there and help the survivors! Why are you just walking away from-?"

"Tails…" Sonic cut him off, swallowing the lump in his throat down and trying to speak again. "…there aren't any survivors, little bro. There's no point in going down there."

"But… we need to try, don't we? Someone must have made it…" The words sounded pitiful even to Tails, and Sonic could only shake his head. The young fox lowered his head, tears brimming in his eyes. They had never had to deal with a tragedy like this in all their fights against Eggman before; always, the conflicts had stopped just before they turned into something ugly. That was clearly not the case here, however.

Sonic brushed past Tails, heading towards the _Tornado_ as he called over his shoulder, "C'mon, Tails, let's get going. We need to start looking for Eggman, pronto. I want to know what he did here."

The young fox followed him, asking in downtrodden confusion, "Sonic, didn't you just say that no one could've… you know…?" Tails was quiet for a moment as he climbed back into the Tornado, sorrow making it difficult for the fox to speak as he got behind the controls of his biplane and Sonic climbed onto his usual spot on the wing. Eventually, he found his voice again, asking, "You don't think Eggman actually got out of there, do you?"

"He always survives," Sonic said flatly. "And I doubt he stuck around after whatever happened here wiped out his fortress, so we'll have to start looking for him elsewhere." The blue hedgehog gazed back towards the billowing smoke rising from the ruined valley, the red clouds still swirling overhead. "I just hope we can catch him before…"

Tails was fiddling with the controls of the plane and not paying complete attention, but when Sonic's voice drifted off into silence the fox looked around, only to see his friend staring up at the sky in shock. "What're you…?" Tails began to ask, before his eyes found what Sonic's had a moment ago.

From within the red mass that hung above the smoldering remains of Eggman's hideout, multiple dark shapes were solidifying, becoming clearer every second. Only a moment after Sonic and Tails had spotted them, the figures burst through the red clouds, flying through the sky at an incredible speed. They quickly sped off towards the horizon, but not before Sonic got a good look at them- a dozen or so aircraft that all looked nearly twice the size of the _Tornado_, with hulls so sleek and rounded that they seemed almost organic in nature. The ships almost resembled teardrops in the way they were tapered from a wide front to a more narrow rear section. They were all black as pitch, with the notable exception of the two larger craft in the center of the formation, which were bulkier in the back and had odd red markings on their sides. The distance and speed of the strange aircraft made it impossible to determine anything else about them, and they had all become small blotches on the horizon even as Sonic tapped Tails on the shoulder and told him, "Get this thing moving, Tails! We've gotta get after them!"

"Sonic, those were nothing like Eggman's ships!" Tails retorted, even as he got the Tornado's rotors spinning and started pulling back on the yoke as the plane started rolling forward, picking up speed quickly. "We have no idea what's really going on here, and you want to just chase after a bunch of weird planes instead of tracking down Eggman? After everything you just said?"

The blue hedgehog pointed one arm at the red clouds. "Tails, have you _ever _seen weather like that before?" Sonic asked in annoyance. "Eggman's base gets annihilated at the exact same time that some freak storm emerges over it, and then a bunch of ships that, as you said, are clearly not Eggman's fly out of it? I only suggested that an accident by the doctor did all this because nothing else seemed reasonable! Here's a new idea- maybe whoever's flying those ships did this? And if they did…" A dangerous scowl appeared on Sonic's face, the kind of expression he only wore when he was deadly serious. "… They might do it again. And I _won't_ let them hurt anyone else. Let's go."

Tails did not question Sonic again; as the biplane lifted off the ground, its engine roaring, the young fox quickly began looking for the strange ships on his radar, increasing the range of the scan as he quickly realized that the other aircraft were far faster than the Tornado. He stared at the screen, eyes wide in fear, as Sonic yelled over the noise of the wind and the plane's engine, "Where're they headed, bro?!"

_Please, don't let this happen… _Tails prayed fervently, even as he struggled to raise his voice so Sonic could hear him. "Sonic…" he stammered.

"…They're flying straight towards Station Square."

* * *

><p><em>(Yeah, I don't always kill off the big villain in the first chapter, but when I do? I make sure there's something even worse to replace him. And believe me, guys, if you played the Shadow the Hedgehog game, the antagonists from it have had the badassevil factor raised to eleven. For those of you who did NOT play it, you're going to figure out quickly what could be worse than Eggman- a LOT worse. _

_Btw, Station Square is the big city in Sonic Adventure 1 and 2, if any of you don't remember. A city full of a few million people is kind of a bad place for a roaring rampage of destruction to take place, and yet that seems to be how things are shaping up. If you were in Tail's place, you would be worried too. _

_Let me know what you thought of this first piece of my second try at Sonic fanfiction. Or don't, which is also okay. Just be sure to check back in, because I can guarantee that none of you will be prepared for some of the crazier chapters in this story._

_Until next time, guys.)_


	2. Update 2

Update: LE HIATUS INDEFINITE!

So, I'm REALLY struggling to make this story come together. I can't describe how infuriating it is to have so many good ideas and not be able to get them out because the beginning s remains awkward no matter how hard I try to correct it.

I know this is not my best work so far, and that's what bugs me- it's the first idea for a fanfic I've ever had, but it'll probably be the last one I complete. I'm suspending Whispers in the Dark indefinitely while I finish Shadow Catcher, By Your Side, and Stand Against The Tide.

I also have a Code Geass story and One Piece one shot in the works, so those will begin once im done with these first three. ONLY THEN will I attempt to fix this story and bring it to the glory that I envisioned when I began it.

Keep an eye on my other stuff for now, I'm making good progress on all fronts.

Ciao


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